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- PDB-5dx0: Crystal structure of CARM1, sinefungin, and H3 peptide (R17) -

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Basic information

Entry
Database: PDB / ID: 5dx0
TitleCrystal structure of CARM1, sinefungin, and H3 peptide (R17)
Components
  • H3 peptide
  • Histone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / protein-substrate ternary complex
Function / homology
Function and homology information


negative regulation of dendrite development / negative regulation of chromosome condensation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Barr body / regulation of centromere complex assembly / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...negative regulation of dendrite development / negative regulation of chromosome condensation / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / Barr body / regulation of centromere complex assembly / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / pericentric heterochromatin formation / inner kinetochore / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H4R3 methyltransferase activity / histone H3K56 methyltransferase activity / muscle cell differentiation / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / histone H2AQ104 methyltransferase activity / oocyte maturation / nucleosomal DNA binding / histone methyltransferase activity / nucleus organization / positive regulation of transcription by RNA polymerase I / spermatid development / nuclear replication fork / single fertilization / positive regulation of fat cell differentiation / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / response to cAMP / : / Regulation of lipid metabolism by PPARalpha / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / BMAL1:CLOCK,NPAS2 activates circadian expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Activation of gene expression by SREBF (SREBP) / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / : / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / Transcriptional activation of mitochondrial biogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / NoRC negatively regulates rRNA expression / Cytoprotection by HMOX1 / beta-catenin binding / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Transcriptional regulation of white adipocyte differentiation / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / : / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / chromosome, telomeric region / cell population proliferation / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Histone H3.3 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsBoriack-Sjodin, P.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates.
Authors: Boriack-Sjodin, P.A. / Jin, L. / Jacques, S.L. / Drew, A. / Sneeringer, C. / Scott, M.P. / Moyer, M.P. / Ribich, S. / Moradei, O. / Copeland, R.A.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
F: H3 peptide
G: H3 peptide
H: H3 peptide
I: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,22418
Polymers166,1308
Non-polymers2,09410
Water8,251458
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
F: H3 peptide
G: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1129
Polymers83,0654
Non-polymers1,0475
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-29 kcal/mol
Surface area26420 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
H: H3 peptide
I: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1129
Polymers83,0654
Non-polymers1,0475
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-29 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.722, 98.847, 208.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDFGHI

#1: Protein
Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 39623.121 Da / Num. of mol.: 4 / Fragment: catalytic domain (UNP residues 134-479)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFastBac / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Protein/peptide
H3 peptide


Mass: 1909.306 Da / Num. of mol.: 4 / Fragment: UNP residues 14-31 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 4 types, 468 molecules

#3: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 88915 / % possible obs: 89.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.046 / Rrim(I) all: 0.092 / Χ2: 1.035 / Net I/av σ(I): 15.485 / Net I/σ(I): 6.8 / Num. measured all: 309548
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.123.60.64487780.830.3740.7470.97489.9
2.12-2.213.50.49186820.8960.2850.570.98889
2.21-2.313.50.36486320.9450.2120.4231.01588.2
2.31-2.433.50.28686200.9620.1670.3321.02688
2.43-2.583.50.21485760.9810.1250.2481.02287.5
2.58-2.783.50.1585280.9890.0880.1741.07486.7
2.78-3.063.40.09885970.9950.0580.1141.09587.2
3.06-3.513.30.0688540.9970.0360.071.12289.5
3.51-4.423.30.05494440.9970.0320.0641.03394.3
4.42-503.60.032102040.9990.0190.0381.01498.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.625 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 4324 4.9 %RANDOM
Rwork0.2111 ---
obs0.2137 84566 89.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.24 Å2 / Biso mean: 34.821 Å2 / Biso min: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2--0 Å2-0 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11274 0 140 458 11872
Biso mean--35.02 36.52 -
Num. residues----1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911720
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211015
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.95815879
X-RAY DIFFRACTIONr_angle_other_deg0.764325313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31251406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08624.004547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.845151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6351556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21744
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022866
X-RAY DIFFRACTIONr_mcbond_it1.8293.3215644
X-RAY DIFFRACTIONr_mcbond_other1.8283.3215643
X-RAY DIFFRACTIONr_mcangle_it2.7344.9697034
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 301 -
Rwork0.314 5995 -
all-6296 -
obs--86.83 %

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